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CABS-flex 3.0

for Efficient Simulations of Protein and Peptide Structural Flexibility

PDB code or upload PDB/cif file

Project name

Flexibility mode

Chain(s)

Protein pLDDT

No
From PDB
From file

Residue-level flexibility control

Email address

Do not show my job on the results page

Show advanced options

Flexibility restraint settings

Gap

Keep restraints (percentage)

Minimum distance [Å]

Maximum distance [Å]

C-alpha minimum weight

C-alpha maximum weight

Side chain minimum weight

Side chain maximum weight

Add custom restraints

C-alpha distance restraints

Side chain distance restraints

Simulation settings

Number of cycles

Cycles between trajectory frames

Temperature of simulation

Seed for random number generation

Disable centrosymmetric potential

Examples: 1ocy_A - Manual 6un0 - Rigid-pLDDT 2gb1 - Rigid 3lq9_A - Flexible

New CABS-flex enhances AlphaFold model flexibility simulations

CABS-flex method

CABS-flex is a computational method designed for efficient simulations of protein and peptide structural flexibility. It combines coarse-grained modeling with all-atom reconstruction, enabling fast yet accurate simulations of structural dynamics while balancing computational efficiency and molecular detail. The method is particularly suitable for exploring conformational changes in proteins, including flexible loops, binding regions, and intrinsically disordered segments. By simplifying protein representation through a reduced set of pseudo-atoms, CABS-flex significantly lowers computational costs while preserving critical structural features. The simulation results are subsequently presented as an ensemble of all-atom structures, providing a detailed and comprehensive representation of protein flexibility and conformational variability.

What's new?

The CABS-flex web server 3.0 introduces several significant advancements aimed at enhancing the accuracy, scope, and usability of protein and peptide flexibility simulations. One of the key improvements is the integration of AlphaFold pLDDT-derived distance restraints, which significantly boosts simulation accuracy by leveraging predicted structural confidence scores. Additionally, the new version supports expanded peptide modeling capabilities, accommodating both linear and cyclic peptides for broader application in prediction of peptide structure and flexibility. The server also features enhanced all-atom structure quality achieved through the cg2all deep learning-based reconstruction method, ensuring more precise atomic-level models. Furthermore, CABS-flex 3.0 includes new tools for analyzing and visualizing simulation results, enabling users to gain deeper insights into structural flexibility and dynamic conformational changes.

Papers describing functionalities of CABS-flex 3.0 method including previous 2.0 server version

CABS-flex 3.0: An Online Tool for Simulating Protein Structural Flexibility and Peptide Modeling, Nucleic Acids Res, 2025
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures, Nucleic Acids Res, 46:W338–W343, 2018
Exploring protein functions from structural flexibility using CABS-flex modeling Protein Sci, 33(9):e5090, 2024
Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations, Comput Struct Biotechnol J, 23:4350-4356, 2024
Structure prediction of linear and cyclic peptides using CABS-flex, Brief Bioinform, 25(2):bbae003, 2024